chr15:78617197:G>T Detail (hg38) (CHRNA3)

Information

Genome

Assembly Position
hg19 chr15:78,909,539-78,909,539 View the variant detail on this assembly version.
hg38 chr15:78,617,197-78,617,197

HGVS

Type Transcript Protein
RefSeq NM_000743.4:c.268-64C>A
NM_001166694.1:c.268-64C>A
Ensemble ENST00000326828.6:c.268-64C>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.593
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 118503 OMIM
HGNC 1957 HGNC
Ensembl ENSG00000080644 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv53653734 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-07-22 criteria provided, single submitter Urinary bladder, atony of germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.327 Lung Neoplasms We found that four of the variants (rs3829787, rs3841324, rs588765 and rs3743073... BeFree 23011884 Detail
0.001 Non-small cell lung carcinoma These results suggest that the rs3743073 polymorphism in CHRNA3 is predictive fo... BeFree 20234319 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000743.5(CHRNA3):c.268-64C>A AND Urinary bladder, atony of ClinVar Detail
We found that four of the variants (rs3829787, rs3841324, rs588765 and rs3743073) were associated wi... DisGeNET Detail
These results suggest that the rs3743073 polymorphism in CHRNA3 is predictive for lung cancer risk a... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs3743073 dbSNP
Genome
hg38
Position
chr15:78,617,197-78,617,197
Variant Type
snv
Reference Allele
G
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs3743073
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5927
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9933
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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